LAMMPS (11 Aug 2017) ######################################################################## ### Heat conduction analog of periodic Poiseuille flow problem ### ### using energy-conserving DPD (eDPD) simulation ### ### ### ### Created : Zhen Li (zhen_li@brown.edu) ### ### Division of Applied Mathematics, Brown University. ### ### ### ### mDPD system setup follows Fig.12 in the publication: ### ### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### ### "Energy-conserving dissipative particle dynamics with ### ### temperature-dependent properties". J. Comput. Phys., ### ### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### ######################################################################## units lj dimension 3 boundary p p p neighbor 0.2 bin neigh_modify every 1 delay 0 check yes atom_style edpd region edpd block -10 10 -10 10 -5 5 units box create_box 1 edpd Created orthogonal box = (-10 -10 -5) to (10 10 5) 1 by 1 by 1 MPI processor grid create_atoms 1 random 16000 276438 NULL Created 16000 atoms mass 1 1.0 set atom * edpd/temp 1.0 16000 settings made for edpd/temp set atom * edpd/cv 1.0E5 16000 settings made for edpd/cv pair_style edpd 1.58 9872598 #pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 compute mythermo all temp thermo 100 thermo_modify temp mythermo thermo_modify flush yes velocity all create 1.0 432982 loop local dist gaussian fix mvv all mvv/edpd 0.5 fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 timestep 0.01 run 500 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.78 ghost atom cutoff = 1.78 binsize = 0.89, bins = 23 23 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair edpd, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 48.948932 0 50.448838 201.73366 100 1.0069712 43.754293 0 45.264656 199.5369 200 0.98667561 43.716052 0 45.195973 196.72854 300 1.0036944 43.706299 0 45.211746 195.35714 400 1.0024228 43.697014 0 45.200554 197.0062 500 0.99968161 43.687445 0 45.186873 193.80596 Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms Performance: 5346.567 tau/day, 6.188 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 75.106 | 75.106 | 75.106 | 0.0 | 92.95 Neigh | 4.9836 | 4.9836 | 4.9836 | 0.0 | 6.17 Comm | 0.31199 | 0.31199 | 0.31199 | 0.0 | 0.39 Output | 0.00048232 | 0.00048232 | 0.00048232 | 0.0 | 0.00 Modify | 0.29985 | 0.29985 | 0.29985 | 0.0 | 0.37 Other | | 0.09751 | | | 0.12 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14091 ave 14091 max 14091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 749111 ave 749111 max 749111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749111 Ave neighs/atom = 46.8194 Neighbor list builds = 181 Dangerous builds = 0 reset_timestep 0 compute temp all edpd/temp/atom compute ccT all chunk/atom bin/1d y 0.0 1.0 fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile run 500 Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.99968161 43.687397 0 45.186825 196.38426 100 1.0041443 43.668196 0 45.174318 195.38066 200 0.99628392 43.666173 0 45.160505 197.84675 300 1.0029116 43.66224 0 45.166513 199.67414 400 0.99922193 43.64406 0 45.142799 196.94404 500 0.99355431 43.623266 0 45.113505 195.94136 Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms Performance: 5348.242 tau/day, 6.190 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 75.073 | 75.073 | 75.073 | 0.0 | 92.94 Neigh | 4.8786 | 4.8786 | 4.8786 | 0.0 | 6.04 Comm | 0.31086 | 0.31086 | 0.31086 | 0.0 | 0.38 Output | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.00 Modify | 0.4139 | 0.4139 | 0.4139 | 0.0 | 0.51 Other | | 0.09731 | | | 0.12 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14091 ave 14091 max 14091 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 749667 ave 749667 max 749667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749667 Ave neighs/atom = 46.8542 Neighbor list builds = 178 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:02:41